Amber List,
I am attempting to run QM/MM NEB with PM3-PDDG on an RNA system with Amber 10.
Inpcrd files for the starting and ending configuration are each copied 15 times to give a total of 30 images.
My addles.in file is as follows:
file rprm name=(reactant.prmtop) read
file rcrd name=(cat_reactant15X-product15X.inpcrd) pack=30 read
file wprm name=(AA-NEB-30image.prmtop) wovr
file wcrd name=(AA-NEB-30image.inpcrd) wovr
action
omas
pimd
spac numc=30 pick #prt 1 587 done
*EOD
My .in file is as follows:
NVT MD w/ position restraints (5 kcal/molA) and PME (sander)
&cntrl
nmropt = 0,
ntx = 1, irest = 0,
ntpr = 50, ntwx = 50,
ntf = 2, ntb = 0, dielc = 1,
igb = 1,
cut = 15.0, saltcon= 0 , rgbmax =15.0,
imin = 0,
maxcyc = 5000,
ncyc = 1000,
dx0 = 0.1, dxm = 0.5, drms = 0.0001,
nstlim = 1000,
nscm = 1000,
t = 0, dt = 0.002,
temp0 = 300.0, tempi = 300,
ig = 1000,
ntt = 3,
gamma_ln = 100,
vlimit = 20.0,
ntp = 0, pres0 = 1.0,
ntc = 2,
ineb = 1,
skmin = 10, skmax = 10, tmode = 1,
ifqnt = 1
/
&qmmm
qmmask = '.143-156,437-450',
qmcharge = 0,
qmcut = 8.0, qmshake = 0,
qm_theory = 'PM3-PDDG', verbosity = 0,
printcharges = 0, peptide_corr = 0,
writepdb = 1,
dftb_disper = 0
/
&end
I attempt to run the calculation on a linux cluster with amber10 sander.MPI and get the following error at the end of the output file:
| Flags: MPI
*** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
THAT WERE CREATED BY ADDLES, WITH NPARM=1
USE A VERSION COMPILED WITH –DLES
I suspect the problem may be with addles and the prmtop file. The same procedure with addles has worked for amber9 NEB using an MM force field. I attempted to submit this above calculation using only the MM force field as well with amber10 and get the same error in the .out file, so I don’t think this problem is related to the QMMM settings.
Does anyone have suggestions on how I may get PM3-PDDG QMMM NEB to work?
Sincerely,
Keith Van Nostrand
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Received on Fri Jul 10 2009 - 10:10:43 PDT
